Transport of protein through nanoporous membranes is important to several problem, ranging from their purification to many biomedical applications. Molecular simulation of this phenomenon can shed light on the underlying physics of the problem and, hence, provide us with insight for practical applications. We have carried out such simulations in a slit pore, using the discontinuous molecular dynamics (DMD) technique, in order to study the stability and folding of the proteins in the pore. Using a novel combination of the DMD and the Langevin equation, we also study transport of proteins in nanopores. A wide range of temperature was considered, the effect of the pore's size on the folding temperature was studied, and both attractive and repulsive interaction potentials between the proteins and the pore's walls was considered. We have utilized an intermediate-resolution protein model, the so-called PRIME model.